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DNA Replication

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by

Ruth Zhang

on 30 October 2014

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Transcript of DNA Replication

The photocopier...
...Then it hits a stop.
Preparation
Now let's talk about what we need to prepare for the multiplication to occur...
DNA Replication
In General...
Two chain problem
What is replication?
“To replicate”= to make an exact copy of the given original.
In simple words, replication is copying or multiplying.

For example, given only a single item as original…

-After 1 round of “copying”: 2 x original
-After 2 rounds of “copying”: 4 x original
-After 3 rounds of “copying”: 8 x original
-After 4 rounds of “copying”: 16 x original
-etc

original
1st round
2nd round
3rd round
Recall that the two chains coiled with each other are a pair. Chain components are very sticky. Each piece on one chain is "glued" tightly with its match on the other. With the chemical bond "glue", they are too strong to be used.
Also, just like how we usually spell and read from left to right, DNA is "written" and "read" in a certain direction as well.
Strand 1
Strand 2
Chemical bond, the "glue"
Thus, a cutting enzyme (molecular scissors) will come in to rip one section of the pair apart into two single chains.
There we have the two chains separate in one region. We call such regions "open regions". Now we can start working on the open regions on both chains respectively!
Before we actually introduce the "photocopier", we have to make sure that the separate, uncoiled chains do not stick onto themselves.
Some pieces of protein will come to the open sections of the two chains, stick onto them and prevent them from wiggling too much!
Before going into any detail of the process, let's first briefly talk about some basics...
"cut open"
Four different simple units are involved in the process. Due to their each distinct structure, two units can pair with each other and the two others can pair with each other.
base pair
base pair
Two simple units pair together!
The other two also pair together!
But NEITHER from left pair will pair with either from right pair
The chain of these simple units also comes in pair. Coiling together makes them stronger. The two chains in a pair are read and written in opposite directions.
Coiled, run in opposite directions
The coiled chains...

The two simple units who like to pair together will be "glued together" by chemical bond! The unit on one chain will be glued to its pairing unit on the other chain.

The two coiled chains are perfect match for each other, as every unit on one chain will have its match on the other chain.
example region
Chemical bond "glue"
After the original chains are ready to be used, all we need to do is to start building a new chain.
An enzyme comes in and lays on the top of the original chain. This enzyme will put a few reactive units that can be paired with the first few normal simple units (on the original chain). The reactive units, although will be removed and replaced later, are going to help us building the new chain.
Next, another enzyme comes in, to add normal simple units to the end of the reactive simple unit chain. At the same time, the normal simple units will be "glued" to their perfect matches on the original, leading to a new chain pair.

Note: the new units added have to pair with the simple units on the original chain. Thus, the newly formed chain will NOT be the exact copy of the original chain that we work on; it will be the exact copy of the pairing original chain instead.
original chain A
original chain B
adding new units
reactive starting units
(later removed and replaced)
These two will become the same
replacing
A third enzyme comes in to remove the reactive simple units at the very beginning of the new chain, leaving a gap there. It will then fill in the gap with some normal simple units.
A sealing enzyme comes in to connect the replacement units with the units at either side of the gap. This way, our new chain remains continuous.

The four enzymes make our photocopier!
Note that in our previous demonstration, the original chain is read in a certain direction and the simple units are added in the opposite direction. This is denoted by the arrowheads. In previous slides, we only used one chain to demonstrated.
the chain that we worked on (original)
"copy" based on the chain we worked on (copy)
pairing chain (original)
In reality, there should be another chain forming
based on the pairing chain
in opposite direction at the same time. This chain is the exact copy of
the chain that we worked on
.
copy of "the chain that we work on", formed based on the pairing chain (copy)
This "copying the chain pair at the same time" mechanism leads to a problem.

Although the two new copies are formed in opposite directions, the opening of the coiled chains goes in only ONE direction. "Scissors" move in ONE direction.

This means that one of the new chains is formed in the opposite direction of where the "scissors" are moving. This conflict in direction causes it to be processed in fragments. We have to join the fragments together by the sealing enzyme mentioned before.
DNA is a container that stores valuable information for us. It makes us who we are!

What is DNA?
Note that in our graphic demonstration, although both chains are shown, we will only use the original chain A to simplify the process, leaving original chain B unused. In real life, both should be used and the original chain B works in the same way as original chain A!
(what we work on)
Let's first look at the big picture!!
"Circles"
Depending on its "owner" organism, the coiled chains can have two different overall shapes. Their overall shape can either be a straight line, or a circle.
Stops when a full cycle is completed
A protein will sit on the last few units on the circular chain;
These last units act as the "stop sign"
After the stop...
We have two chain pairs that are connected with each other...
1st pair: original chain A + a copy of chain B that is formed on the base of A
How can we separate the two pairs?
2nd pair: original chain B + a copy of chain A that is formed on the base of B
A final cutting enzyme will come in to cut the two pairs apart. This cutting enzyme is different from the one we had before.
"Line"
original
new
In one of the chains, the stop sign is placed on the forward (arrowhead) direction of the original chain.
reactive units that need to be removed
After the reactive units are removed, there will be a gap that we could not fix, because we have already reached the end of the original and we could not fit the "photocopier" on it anymore.
Solution: we lengthen the original a little, so that the "photocopier" can come in and do its work.

This way, we will have a full length copy of the original without losing any information.

After we finish the full length copy, the last bit of additional units on the original strand will fold on itself. These additional units do not contain any useful information and they are just there to provide a place for the photocopier to sit in.
Opening only one section of the chains is not enough for us.

The two chains are cut apart continually in order for the process to proceed.

The "scissors" will slide its way down the coiled chain in a certain direction to ensure the continuity of the process
(original pairing chain)
The photocopier is composed of four enzymes!
Similarly, linear chain pairs also have the "stop sign" simple units. They are located at the very end of the original chain. Protein will come in and sit on the "stop sign", and this will stop the whole process.
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